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RNAseq analysis in R

This workshop was first taught here.

Some of these materials are adapted from the R-novice-gapminder, while subsequent materials were derived from X, with substantial new additions from X, Y, Z.

These lesson materials are designed to be run after a complete introduction to R course (e.g. SWC or DC) or equivalent background knowledge.

Contributing

Please see the current list of issues for ideas for contributing to this repository, and the guidelines and instructions for contributing.

When editing topic pages, you should change the source R Markdown file. Afterwards you can render the pages by running make preview from the base of the repository. Building the rendered page with the Makefile requires installing some dependencies first. In addition to the dependencies listed in the lesson template documentation, you also need to install the R package knitr.

Once you've made your edits and looked over the rendered html files, you should add, commit, and push only the source R Markdown file(s) to your fork, and then open a pull request. The repository maintainers will run the html generation process once the pull request has been merged. You can learn more about the design of the build process here.

Getting Help

These notes refer to SWC help, but note that this workshop has not yet been submitted to SWC or DC. So please use this github repository for any correspondence for now.

Please see https://github.com/swcarpentry/lesson-example for instructions on formatting, building, and submitting lessons, or run make in this directory for a list of helpful commands.

If you have questions or proposals, please send them to the r-discuss mailing list.

Rendered version of lessons

You can also view the rendered version of this material.